Nuclease pre-treatment increases efficiency of whole genome sequencing of Influenza B virus in respiratory specimens
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Published:2020-01-21
Issue:
Volume:
Page:1-13
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ISSN:2672-7277
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Container-title:Asia Pacific Journal of Molecular Biology and Biotechnology
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language:en
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Short-container-title:APJMBB
Author:
Manasatienkij Wudtichai1, Chinnawirotpisan Piyawan2, Kittichotirat Weerayuth3, Simasathien Sriluck4, Macareo Louis R.2, Ellison Damon W.2, Cheevadhanarak Supapon1, Rutvisuttinunt Wiriya2, Fernandez Stefan2, Klungthong Chonticha2
Affiliation:
1. Biotechnology Division, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand 2. Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand 3. Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand 4. Phramongkutklao Hospital, Bangkok, Thailand
Abstract
The use of next generation sequencing (NGS) directly on respiratory specimens to obtain viral whole genome sequence (WGS) enhances the capability for rapid and unbiased viral characterization. One of the challenges of using NGS directly in influenza-like illness (ILI) respiratory specimens is the higher proportion of host and bacterial genome compared to viral genetic materials found, which reduces the likelihood of obtaining complete viral genome sequences. This study aims to evaluate nuclease pretreatments prior to sequencing of influenza B virus directly from ILI respiratory specimens. Sequence data were mapped to human, bacteria and influenza B viral genome. In the absence of any nuclease pretreatments, the sequence reads identified as Haemophilus influenzae, Haemophilus parainfluenzae, Neisseria meningitidis and Veillonella parvula were the most prominent genetic materials in respiratory specimens. Filtration followed by nuclease treatment reduced bacterial sequence reads by at least 70 folds in all 4 tested samples, supporting the direct application of NGS in ILI respiratory specimens. Although the pretreatment methods significantly reduced human genome sequences, the remaining human genome especially human rRNA still impact the number and proportion of the viral sequence reads.
Publisher
Malaysian Society for Molecular Biology and Biotechnology
Subject
Molecular Biology,Biotechnology
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